NCBI批量下载基因组

#!/usr/bin/python
#author: W.-S. Zheng
#date 20180429
# -*- coding: UTF-8 -*-
#usage: download genomes from ncbi database

import glob
from ftplib import FTP
import os
import sys

# ------------------- 类和函数定义 -----------------------
class MyPathes:
    '''定义类储存当前路径，当前路径下的文件名，当前路径下的文件夹名'''

    def __init__(self, cur_path, ftp):
        self.cur = cur_path
        self.ftp = ftp
        self.folders = []
        self.files = []
        self.nextPathes = []
        self.links = []

        self.content = self.getContet()
        self.sort()
        self.createPathes()

    def getContet(self):
        dir_content = []
        self.ftp.cwd(self.cur)
        self.ftp.retrlines('LIST', callback = dir_content.append)
        return dir_content

    def sort(self):
        for line in self.content:
            if line.startswith('d'):
                self.folders.append(line.split(" ")[-1])
            elif line.startswith('l'):
                self.links.append(line.split(" ")[-1])
            else:
                self.files.append(line.split(" ")[-1])

    def oneDes(self):
        return(len(self.folders) == 1)


    def createPathes(self):
        for folder in self.folders:
            self.nextPathes.append(self.cur + '/' + folder)
        return(self.nextPathes)

# -------------------------下载 -----------------------------
# 转换accession no. 为路径
def acc2path(acc):
    root = '/genomes/all/GCA/'
    acc = acc.split('_')[1]
    acc = acc.split('.')[0]
    path = root + acc[0:3] + '/' + acc[3:6] + '/' + acc[6:9]
    return path

# 连接FTP
def con():
    ftp = FTP()
    ftp.connect("ftp.ncbi.nlm.nih.gov", 21)
    ftp.login()#连接的用户名，密码
    return(ftp)

# 下载文件
def downloadFile(filename):
    try:
        ftp.retrbinary("RETR " + filename, open(filename, 'wb').write)
    except FileExistsError:
        pass

# 下载文件夹
def downloadFolder(dir_folder):
    try:
        os.mkdir(dir_folder)
    except FileExistsError:
        print('File existed')
    os.chdir(dir_folder)



# 获得GenBank No.
# 存在同文件夹中，唯一的txt文件中
file = glob.glob('*.txt')
print(file)
accessions = open(file[0], 'r').readlines()
print(accessions)


# 逐个下载，适用于文件夹中不包括其他文件夹
for acc in accessions:
    os.chdir('E://')

    # 将No解析为路径
    root = acc2path(acc)
    print(root)


    # 连接FTP
    ftp = con()

    # 解析当前路径的内容
    x1 = MyPathes(root, ftp)

    # 进入要下载的文件夹
    # 如果不只一个版本提醒
    if not x1.oneDes():
        print("More than one version available!")

    else:
        # 连接FTP
        ftp = con()
        # 建立本地文件夹
        downloadFolder(x1.folders[0])
        # 进入下一级ftp目录
        x2 = MyPathes(x1.nextPathes[0], ftp)

        # 开始下载
        print('start!')
        prog = len(x2.files)
        for file in x2.files:
            downloadFile(file)
            sys.stdout.write("%i=" % (prog))
            sys.stdout.flush()
            prog = prog-1

        if not x2.nextPathes:
            print('Done')
        else:
            print('Must go deeper')